Ciprofloxacin-driven purifying selection on viral genomes accelerates soil N₂O production

Viruses are ubiquitous regulators of microbial dynamics and may thus greatly influence global microbial-driven greenhouse gas emissions. Anthropogenic stressors, such as chemical contamination, are likely to amplify these viral contributions; however, their global significance and underlying mechanisms remain elusive. Utilizing ¹⁵N tracing, metagenomics, and laboratory assays, we explore soil viral communities and their evolutionary potential under the stress from antibiotic ciprofloxacin (CIP), focusing on their roles in regulating nitrogen cycling and N₂O production. Through isolation and reinoculation of soil viruses, we demonstrate that CIP stimulates soil denitrification-derived N₂O production, with 18 to 29% of the increase attributed to viral activity. Under CIP stress, soil viruses shift toward a lysogenic lifestyle, promoting mutualism with denitrifiers by horizontally transferring viral denitrification-related auxiliary metabolic genes (AMGs). The observed synonymous mutations in these AMGs, driven by CIP, suggest enhanced purifying selection, likely optimizing codon usage to align with host preferences. This optimization likely enhances the expression of denitrifying AMGs and increases N₂O production. This study provides insights into the overlooked role of viral dynamics and genomic mutations in modulating N₂O production under stressful environments, highlighting their evolutionary significance and impact on biogeochemical cycles in the Anthropocene.